We have developed a three-dimensional multi-layred optical strage system. The system records pits into the thick material in three dimensions along the optical axis direction. For recording, we used photorefractive materials such as photopolymer and photorefractive crystal (LiNbO_3), which are used in volume holographic recording. Pits are recorded as refractive index changes. We employed a laser scanning microscope to record and access the pits. The scanning microscope allows us to record and read multi-layred data. We employed in combination a phase contrast microscope for imaging refractive index distribution and a confocal microscope to reduce unwanted scattered light particularly during reading. By using 40x, N.A = 1.0, oil immersion type objective lens and Ar+laser, bit data were written every 2mum x 2mum at 50 x 50 bits per plane. A total of thirty planes was recorded at a longitudinal separation distance of 10mum between plane.We analyze the three-dimensional refractive-index distribution that is induced locally when a laser beam is focused unto a very small region in a photorefractive crystal. The formation of the index distribution is deduced from the temporal behavior of the electron density distribution in the crystal under non-steady state conditions. The density distribution is computed using a set of the recurrence relations that were derived from Kukhtarev's equations describing the transport of electrons in time. In particular, we calculated the index distribution formed in Fe-doped LiNbO_3 crystals. To verify the validity of our analysis, we read using a phase contrast microscope, refractive index dots that were recorded in Fe-doped LiNbO_3 crystals. A good agreement was obtained between experimental results and the calculated phase contrast image when the characteristics of the imaging system is taken into account.